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I have done my second reading of AGoT, and I started to think that it was Lysa who poisoned Lord Jon Arryn. All this misunderstanding with Robert's fostering place, means something. I have not read last three books, so I am looking forward to to find out if I was right :)

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Jon Arryn had been investigating together with Stannis, and upon discovering the truth about Cersei and her children, Jon Arryn had decided that Lysa would be returning to the Eyrie, and Robert Arryn would go to Dragonstone, to be fostered by Stannis.

The decision about his son had an impact on Jon Arryn which will be revealed in a further novel ;) keep reading.

After Jon's death, Robert Baratheon, seening how weak and sickly his namesake was under his mothers care, negotiated with Tywin Lannister for sweetrobin to be fostered at Casterly Rock, to which Tywin agreed. That news did not sit well with Lysa, who fled in the night back to the Eyrie in response.

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My only thoughts of this were that what Jon Arryn said about "The Seed Was Strong" was about all of Robberts and other Baratheon children inherited the black hair and deep blue eyes genes being strong.

The confusion between little Robberts fostering was that Jon wanted him to be fostered at Dragon Stone and Lisa strongly disliking the idea and it caused friction but after his death King Rob wanted to send him to Casterly Rock instead under pressure from Lannisters who wanted little Rob in their custardy, which Lise liked even less. I came to this decision after rereading that everybody who spoke to Jon Arryn said Dragon Stone, Walder Frey, the Maester Colemon and King Rob, Catelyn after the King announced it.

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Although I am on my re-read of AGoT, I have always thought that "the seed is strong" had a dual meaning. Jon Arryn was a very intelligent man, and there were two persons there on his death bed, his wife Lysa and King Robert Baratheon who would have needed to hear the words. It's a message that speaks to both of them, and Jon likely carefully intended it that way.

It is clear that the subject of fostering Robert Arryn was a source of discord between Jon and Lysa, her reasoning being that her son was far too weak and fragile. Jon had reasons to both want Robert Arryn away from King's Landing, perhaps assuring Lysa that the seed is strong was his way of indicating that fostering him was fine. Of course, the true heart of the message was for Robert Baratheon in hopes that the king would discover the truth about Joffrey, Myrcella, and Tommen, but that's not to say it wasn't meant for both of them, just in different contexts.

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I believe that Jons final words of 'The seed is strong' is to mean the Baratheon genes. As when Ned is reading the traits of the Baratheon family line he states that hey a have black of hair. It is well known that Robert has fathered many bastards, all of which have the black hair of the Baratheon house.
I highly doubt that his last words were about himself as all attempts at conceiving a baby with Lysa had failed with the exception of on one occasion when Robert Arryn was born.

Jon Arryn and Stannis were together throughout most of Jons investigations into Roberts bastards and we can assume that they grew fairly close. Maybe during a discussion with Stannis about the disappointment of a son that he fathered who will one day become the Lord of the Vale and warden of the east, Stannis perhaps suggests that he will foster the boy himself as we all come to learn that Stannis can be a hard person to live under. He would give the necessary guidance to lead Robert to becoming a worthy heir.
All of this however, was not widely known and as we know that when Jon died, King Robert planned to foster him at the rock with Lord Tywin which was probably down to Cerseis whisperings into his ear. As Tywin has never fostered before, this would be more likely to pass around on the tongues of the small folk.

When Tyrions trial is about to take place at the Eyrie, Maester Colemon begins to tell Catelyn of Jons plans to foster the boy at Dragonstone but is interrupted by the trial beginning.

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They were not friends. They were corgel to one another, Stannis respected him and vice versa but i don't think Stannis has friends...

They discovered a plot against Robbert and were working together to investigate i imagine Jon was sending Little Robert to DragonStone to foster so he could learn from Stannis but i think it was a sign of trust, a strengthening of their little alliance against the Lannisters.

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I dont think its about health at all, its about mental kind of things. Lysa Arryn is all crazy about him, so it also developed into health problems. You are right that it was the best possible way for little Robert, would have been very interesting how the story would develop if this happened